Using chromatin immunoprecipitation to map cotranscriptional mRNA processing in Saccharomyces cerevisiae

Methods Mol Biol. 2004;257:1-16. doi: 10.1385/1-59259-750-5:001.

Abstract

The chromatin immunoprecipitation (ChIP) technique has been used to determine where and under what conditions DNA binding proteins associate with specific DNA sequences. Proteins are crosslinked in vivo with formaldehyde, and chromatin is then isolated and sheared. The protein of interest is then immunoprecipitated and the associated DNA sequences identified via PCR. Although this technique was originally designed to assay DNA binding proteins, it can also be used to monitor mRNA processing factors associated with transcription complexes.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Chromatin / genetics*
  • Chromatin / isolation & purification
  • Chromosomes, Fungal / genetics
  • Cross-Linking Reagents
  • DNA, Fungal / genetics
  • DNA, Fungal / isolation & purification
  • DNA, Fungal / metabolism
  • Formaldehyde / metabolism
  • Polymerase Chain Reaction
  • Precipitin Tests / methods*
  • RNA Processing, Post-Transcriptional*
  • RNA, Fungal
  • RNA, Messenger / metabolism*
  • RNA-Binding Proteins / metabolism
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism
  • Transcription Factors / metabolism
  • Transcription, Genetic

Substances

  • Chromatin
  • Cross-Linking Reagents
  • DNA, Fungal
  • RNA, Fungal
  • RNA, Messenger
  • RNA-Binding Proteins
  • Saccharomyces cerevisiae Proteins
  • Transcription Factors
  • Formaldehyde